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Protein

Phosphoglycerate mutase 1

Gene

GPM1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Interconversion of 3- and 2-phosphoglycerate with 2,3-bisphosphoglycerate as the primer of the reaction. Can also Catalyzes the reaction of EC 5.4.2.4 (synthase), but with a reduced activity.2 Publications

Miscellaneous

Present with 172000 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

2-phospho-D-glycerate = 3-phospho-D-glycerate.1 Publication

Activity regulationi

Inhibited by inositol hexakisphosphate and benzene tri-, tetra- and hexacarboxylates.1 Publication

Kineticsi

kcat is 490 sec(-1) for the mutase reaction, 0.0074 sec(-1) for the synthase reaction and 0.0087 sec(-1) for the phosphatase reaction with 3-phosphoglycerate as substrate.1 Publication
  1. KM=740 µM for 3-phosphoglycerate2 Publications
  2. KM=8.1 µM for 2,3-bisphosphoglycerate (for mutase reaction)2 Publications
  3. KM=2.4 µM for 2,3-bisphosphoglycerate (for phosphatase reaction)2 Publications

    Pathwayi: glycolysis

    This protein is involved in step 3 of the subpathway that synthesizes pyruvate from D-glyceraldehyde 3-phosphate.
    Proteins known to be involved in the 5 steps of the subpathway in this organism are:
    1. Glyceraldehyde-3-phosphate dehydrogenase 1 (TDH1), Glyceraldehyde-3-phosphate dehydrogenase 2 (TDH2), Glyceraldehyde-3-phosphate dehydrogenase 3 (TDH3)
    2. Phosphoglycerate kinase (PGK1)
    3. Phosphoglycerate mutase 2 (GPM2), Phosphoglycerate mutase 3 (GPM3), Phosphoglycerate mutase 1 (GPM1)
    4. Enolase 2 (ENO2), Enolase-related protein 2 (ERR2), Enolase 1 (ENO1), Enolase-related protein 3 (ERR3), Enolase-related protein 1 (ERR1)
    5. Pyruvate kinase 1 (CDC19), Pyruvate kinase 2 (PYK2)
    This subpathway is part of the pathway glycolysis, which is itself part of Carbohydrate degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyruvate from D-glyceraldehyde 3-phosphate, the pathway glycolysis and in Carbohydrate degradation.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei9Tele-phosphohistidine intermediate4 Publications1
    Binding sitei60Substrate1 Publication1
    Active sitei87Proton donor/acceptor1 Publication1
    Binding sitei98Substrate1 Publication1
    Sitei182Transition state stabilizer1 Publication1

    GO - Molecular functioni

    GO - Biological processi

    • gluconeogenesis Source: SGD
    • glycolytic process Source: SGD
    • regulation of pentose-phosphate shunt Source: GO_Central

    Keywordsi

    Molecular functionIsomerase
    Biological processGlycolysis

    Enzyme and pathway databases

    BioCyciMetaCyc:YKL152C-MONOMER
    YEAST:YKL152C-MONOMER
    BRENDAi5.4.2.11 984
    ReactomeiR-SCE-6798695 Neutrophil degranulation
    R-SCE-70171 Glycolysis
    R-SCE-70263 Gluconeogenesis
    SABIO-RKiP00950
    UniPathwayi
    UPA00109;UER00186

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Phosphoglycerate mutase 1 (EC:5.4.2.111 Publication)
    Short name:
    PGAM 1
    Alternative name(s):
    BPG-dependent PGAM 1
    MPGM 1
    Phosphoglyceromutase 1
    Gene namesi
    Name:GPM1
    Synonyms:GPM
    Ordered Locus Names:YKL152C
    ORF Names:YKL607
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome XI

    Organism-specific databases

    EuPathDBiFungiDB:YKL152C
    SGDiS000001635 GPM1

    Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

    Keywords - Cellular componenti

    Cytoplasm, Membrane, Mitochondrion, Mitochondrion outer membrane

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi169K → P: Causes dissociation of the homotetramer to dimers at low concentrations. 1 Publication1
    Mutagenesisi182H → A: Reduces kcat of the mutase reaction 10000-fold. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00001798392 – 247Phosphoglycerate mutase 1Add BLAST246

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei12PhosphoserineCombined sources1
    Cross-linki31Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Modified residuei49PhosphotyrosineCombined sources1
    Cross-linki57Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Cross-linki71Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Modified residuei116PhosphoserineCombined sources1
    Modified residuei127PhosphoserineCombined sources1
    Modified residuei128PhosphoserineCombined sources1
    Cross-linki139Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Cross-linki175Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Modified residuei185PhosphoserineCombined sources1
    Cross-linki191Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Modified residuei197PhosphoserineCombined sources1

    Keywords - PTMi

    Isopeptide bond, Phosphoprotein, Ubl conjugation

    Proteomic databases

    MaxQBiP00950
    PaxDbiP00950
    PRIDEiP00950
    TopDownProteomicsiP00950

    2D gel databases

    COMPLUYEAST-2DPAGEiP00950
    SWISS-2DPAGEiP00950

    PTM databases

    iPTMnetiP00950

    Interactioni

    Subunit structurei

    Homotetramer: dimer of dimers.6 Publications

    Protein-protein interaction databases

    BioGridi33985, 76 interactors
    DIPiDIP-6260N
    IntActiP00950, 115 interactors
    MINTiP00950
    STRINGi4932.YKL152C

    Structurei

    Secondary structure

    1247
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    ProteinModelPortaliP00950
    SMRiP00950
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00950

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni8 – 15Substrate binding3 Publications8
    Regioni21 – 22Substrate binding2 Publications2
    Regioni87 – 90Substrate binding2 Publications4
    Regioni114 – 115Substrate binding1 Publication2
    Regioni183 – 184Substrate binding2 Publications2

    Compositional bias

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Compositional biasi233 – 242Ala-rich10

    Sequence similaritiesi

    Phylogenomic databases

    GeneTreeiENSGT00390000016700
    HOGENOMiHOG000221682
    InParanoidiP00950
    KOiK01834
    OMAiRMLPYWY
    OrthoDBiEOG092C4JJL

    Family and domain databases

    CDDicd07067 HP_PGM_like, 1 hit
    Gene3Di3.40.50.1240, 1 hit
    HAMAPiMF_01039 PGAM_GpmA, 1 hit
    InterProiView protein in InterPro
    IPR013078 His_Pase_superF_clade-1
    IPR029033 His_PPase_superfam
    IPR001345 PG/BPGM_mutase_AS
    IPR005952 Phosphogly_mut1
    PANTHERiPTHR11931 PTHR11931, 1 hit
    PfamiView protein in Pfam
    PF00300 His_Phos_1, 1 hit
    SMARTiView protein in SMART
    SM00855 PGAM, 1 hit
    SUPFAMiSSF53254 SSF53254, 1 hit
    TIGRFAMsiTIGR01258 pgm_1, 1 hit
    PROSITEiView protein in PROSITE
    PS00175 PG_MUTASE, 1 hit

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P00950-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MPKLVLVRHG QSEWNEKNLF TGWVDVKLSA KGQQEAARAG ELLKEKKVYP
    60 70 80 90 100
    DVLYTSKLSR AIQTANIALE KADRLWIPVN RSWRLNERHY GDLQGKDKAE
    110 120 130 140 150
    TLKKFGEEKF NTYRRSFDVP PPPIDASSPF SQKGDERYKY VDPNVLPETE
    160 170 180 190 200
    SLALVIDRLL PYWQDVIAKD LLSGKTVMIA AHGNSLRGLV KHLEGISDAD
    210 220 230 240
    IAKLNIPTGI PLVFELDENL KPSKPSYYLD PEAAAAGAAA VANQGKK
    Length:247
    Mass (Da):27,609
    Last modified:January 23, 2007 - v3
    Checksum:i45E1A9CCDBDC104D
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X06408 Genomic DNA Translation: CAA29698.1
    X58789 Genomic DNA Translation: CAA41595.1
    Z26877 Genomic DNA Translation: CAA81501.1
    Z28152 Genomic DNA Translation: CAA81994.1
    S57976 Genomic DNA Translation: AAB26026.1 Different termination.
    BK006944 Genomic DNA Translation: DAA09011.1
    PIRiS00358 PMBYY
    RefSeqiNP_012770.1, NM_001179718.1

    Genome annotation databases

    EnsemblFungiiYKL152C; YKL152C; YKL152C
    GeneIDi853705
    KEGGisce:YKL152C

    Similar proteinsi

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X06408 Genomic DNA Translation: CAA29698.1
    X58789 Genomic DNA Translation: CAA41595.1
    Z26877 Genomic DNA Translation: CAA81501.1
    Z28152 Genomic DNA Translation: CAA81994.1
    S57976 Genomic DNA Translation: AAB26026.1 Different termination.
    BK006944 Genomic DNA Translation: DAA09011.1
    PIRiS00358 PMBYY
    RefSeqiNP_012770.1, NM_001179718.1

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1BQ3X-ray2.70A/B/C/D2-247[»]
    1BQ4X-ray2.50A/B/C/D2-247[»]
    1QHFX-ray1.70A/B2-241[»]
    3PGMX-ray2.80A/B2-247[»]
    4PGMX-ray2.30A/B/C/D2-247[»]
    5PGMX-ray2.12A/B/C/D/E/F/G/H2-247[»]
    ProteinModelPortaliP00950
    SMRiP00950
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi33985, 76 interactors
    DIPiDIP-6260N
    IntActiP00950, 115 interactors
    MINTiP00950
    STRINGi4932.YKL152C

    PTM databases

    iPTMnetiP00950

    2D gel databases

    COMPLUYEAST-2DPAGEiP00950
    SWISS-2DPAGEiP00950

    Proteomic databases

    MaxQBiP00950
    PaxDbiP00950
    PRIDEiP00950
    TopDownProteomicsiP00950

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYKL152C; YKL152C; YKL152C
    GeneIDi853705
    KEGGisce:YKL152C

    Organism-specific databases

    EuPathDBiFungiDB:YKL152C
    SGDiS000001635 GPM1

    Phylogenomic databases

    GeneTreeiENSGT00390000016700
    HOGENOMiHOG000221682
    InParanoidiP00950
    KOiK01834
    OMAiRMLPYWY
    OrthoDBiEOG092C4JJL

    Enzyme and pathway databases

    UniPathwayi
    UPA00109;UER00186

    BioCyciMetaCyc:YKL152C-MONOMER
    YEAST:YKL152C-MONOMER
    BRENDAi5.4.2.11 984
    ReactomeiR-SCE-6798695 Neutrophil degranulation
    R-SCE-70171 Glycolysis
    R-SCE-70263 Gluconeogenesis
    SABIO-RKiP00950

    Miscellaneous databases

    EvolutionaryTraceiP00950
    PROiPR:P00950

    Family and domain databases

    CDDicd07067 HP_PGM_like, 1 hit
    Gene3Di3.40.50.1240, 1 hit
    HAMAPiMF_01039 PGAM_GpmA, 1 hit
    InterProiView protein in InterPro
    IPR013078 His_Pase_superF_clade-1
    IPR029033 His_PPase_superfam
    IPR001345 PG/BPGM_mutase_AS
    IPR005952 Phosphogly_mut1
    PANTHERiPTHR11931 PTHR11931, 1 hit
    PfamiView protein in Pfam
    PF00300 His_Phos_1, 1 hit
    SMARTiView protein in SMART
    SM00855 PGAM, 1 hit
    SUPFAMiSSF53254 SSF53254, 1 hit
    TIGRFAMsiTIGR01258 pgm_1, 1 hit
    PROSITEiView protein in PROSITE
    PS00175 PG_MUTASE, 1 hit
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPMG1_YEAST
    AccessioniPrimary (citable) accession number: P00950
    Secondary accession number(s): D6VX45, Q02117
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: January 23, 2007
    Last modified: September 12, 2018
    This is version 205 of the entry and version 3 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome XI
      Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names
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